Unifying Parsimonious Tree Reconciliation

Evolution is a process that is influenced by various environmental factors, e.g. the interactions between different species, genes, and biogeographical properties. Hence, it is interesting to study the combined evolutionary history of multiple species, their genes, and the environment they live in. A common approach to address this research problem is to describe each individual evolution as a phylogenetic tree and construct a tree reconciliation which is parsimonious with respect to a given event model. Unfortunately, most of the previous approaches are designed only either for host-parasite systems, for gene tree/species tree reconciliation, or biogeography. Hence, a method is desirable, which addresses the general problem of mapping phylogenetic trees and covering all varieties of coevolving systems, including e.g., predator-prey and symbiotic relationships. To overcome this gap, we introduce a generalized cophylogenetic event model considering the combinatorial complete set of local coevolutionary events. We give a dynamic programming based heuristic for solving the maximum parsimony reconciliation problem in time O(n^2), for two phylogenies each with at most n leaves. Furthermore, we present an exact branch-and-bound algorithm which uses the results from the dynamic programming heuristic for discarding partial reconciliations. The approach has been implemented as a Java application which is freely available from http://pacosy.informatik.uni-leipzig.de/coresym.Comment: Peer-reviewed and presented as part of the 13th Workshop on Algorithms in Bioinformatics (WABI2013

Biodiversity informatics: the challenge of linking data and the role of shared identifiers

A major challenge facing biodiversity informatics is integrating data stored in widely distributed databases. Initial efforts have relied on taxonomic names as the shared identifier linking records in different databases. However, taxonomic names have limitations as identifiers, being neither stable nor globally unique, and the pace of molecular taxonomic and phylogenetic research means that a lot of information in public sequence databases is not linked to formal taxonomic names. This review explores the use of other identifiers, such as specimen codes and GenBank accession numbers, to link otherwise disconnected facts in different databases. The structure of these links can also be exploited using the PageRank algorithm to rank the results of searches on biodiversity databases. The key to rich integration is a commitment to deploy and reuse globally unique, shared identifiers (such as DOIs and LSIDs), and the implementation of services that link those identifiers

Prospects of Detecting Baryon and Quark Superfluidity from Cooling Neutron Stars

Baryon and quark superfluidity in the cooling of neutron stars are investigated. Observations could constrain combinations of the neutron or Lambda-hyperon pairing gaps and the star's mass. However, in a hybrid star with a mixed phase of hadrons and quarks, quark gaps larger than a few tenths of an MeV render quark matter virtually invisible for cooling. If the quark gap is smaller, quark superfluidity could be important, but its effects will be nearly impossible to distinguish from those of other baryonic constituents.Comment: 4 pages, 3 ps figures, uses RevTex(aps,prl). Submitted to Phys. Rev. Let

Agnesi Weighting for the Measure Problem of Cosmology

The measure problem of cosmology is how to assign normalized probabilities to observations in a universe so large that it may have many observations occurring at many different spacetime locations. I have previously shown how the Boltzmann brain problem (that observations arising from thermal or quantum fluctuations may dominate over ordinary observations if the universe expands sufficiently and/or lasts long enough) may be ameliorated by volume averaging, but that still leaves problems if the universe lasts too long. Here a solution is proposed for that residual problem by a simple weighting factor 1/(1+t^2) to make the time integral convergent. The resulting Agnesi measure appears to avoid problems other measures may have with vacua of zero or negative cosmological constant.Comment: 26 pages, LaTeX; discussion is added of how Agnesi weighting appears better than other recent measure

Cosmological Measures without Volume Weighting

Many cosmologists (myself included) have advocated volume weighting for the cosmological measure problem, weighting spatial hypersurfaces by their volume. However, this often leads to the Boltzmann brain problem, that almost all observations would be by momentary Boltzmann brains that arise very briefly as quantum fluctuations in the late universe when it has expanded to a huge size, so that our observations (too ordered for Boltzmann brains) would be highly atypical and unlikely. Here it is suggested that volume weighting may be a mistake. Volume averaging is advocated as an alternative. One consequence may be a loss of the argument that eternal inflation gives a nonzero probability that our universe now has infinite volume.Comment: 15 pages, LaTeX, added references for constant-H hypersurfaces and also an idea for minimal-flux hypersurface

A window into the neutron star: Modelling the cooling of accretion heated neutron star crusts

In accreting neutron star X-ray transients, the neutron star crust can be substantially heated out of thermal equilibrium with the core during an accretion outburst. The observed subsequent cooling in quiescence (when accretion has halted) offers a unique opportunity to study the structure and thermal properties of the crust. Initially crust cooling modelling studies focussed on transient X-ray binaries with prolonged accretion outbursts (> 1 year) such that the crust would be significantly heated for the cooling to be detectable. Here we present the results of applying a theoretical model to the observed cooling curve after a short accretion outburst of only ~10 weeks. In our study we use the 2010 outburst of the transiently accreting 11 Hz X-ray pulsar in the globular cluster Terzan 5. Observationally it was found that the crust in this source was still hot more than 4 years after the end of its short accretion outburst. From our modelling we found that such a long-lived hot crust implies some unusual crustal properties such as a very low thermal conductivity (> 10 times lower than determined for the other crust cooling sources). In addition, we present our preliminary results of the modelling of the ongoing cooling of the neutron star in MXB 1659-298. This transient X-ray source went back into quiescence in March 2017 after an accretion phase of ~1.8 years. We compare our predictions for the cooling curve after this outburst with the cooling curve of the same source obtained after its previous outburst which ended in 2001.Comment: 4 pages, 1 figure, to appear in the proceedings of "IAUS 337: Pulsar Astrophysics - The Next 50 Years" eds: P. Weltevrede, B.B.P. Perera, L. Levin Preston & S. Sanida

Going nuclear: gene family evolution and vertebrate phylogeny reconciled

Gene duplications have been common throughout vertebrate evolution, introducing paralogy and so complicating phylogenctic inference from nuclear genes. Reconciled trees are one method capable of dealing with paralogy, using the relationship between a gene phylogeny and the phylogeny of the organisms containing those genes to identify gene duplication events. This allows us to infer phylogenies from gene families containing both orthologous and paralogous copies. Vertebrate phylogeny is well understood from morphological and palaeontological data, but studies using mitochondrial sequence data have failed to reproduce this classical view. Reconciled tree analysis of a database of 118 vertebrate gene families supports a largely classical vertebrate phylogeny

Opaque or transparent? A link between neutrino optical depths and the characteristic duration of short gamma-ray bursts

Cosmological gamma ray bursts (GRBs) are thought to occur from violent hypercritical accretion onto stellar mass black holes, either following core collapse in massive stars or compact binary mergers. This dichotomy may be reflected in the two classes of bursts having different durations. Dynamical calculations of the evolution of these systems are essential if one is to establish characteristic, relevant timescales. We show here for the first time the result of dynamical simulations, lasting approximately one second, of post--merger accretion disks around black holes, using a realistic equation of state and considering neutrino emission processes. We find that the inclusion of neutrino optical depth effects produces important qualitative temporal and spatial transitions in the evolution and structure of the disk, which may directly reflect upon the duration and variability of short GRBs.Comment: Accepted for publication in ApJ Letter

What Have We Learned from Policy Transfer Research? Dolowitz and Marsh Revisited

Over the last decade, policy transfer has emerged as an important concept within public policy analysis, guiding both theoretical and empirical research spanning many venues and issue areas. Using Dolowitz and Marsh's 1996 stocktake as its starting point, this article reviews what has been learned by whom and for what purpose. It finds that the literature has evolved from its rather narrow, state-centred roots to cover many more actors and venues. While policy transfer still represents a niche topic for some researchers, an increasing number have successfully assimilated it into wider debates on topics such as globalisation, Europeanisation and policy innovation. This article assesses the concept's position in the overall ‘tool-kit’ of policy analysis, examines some possible future directions and reflects on their associated risks and opportunities

Transient Observers and Variable Constants, or Repelling the Invasion of the Boltzmann's Brains

If the universe expands exponentially without end, ``ordinary observers'' like ourselves may be vastly outnumbered by ``Boltzmann's brains,'' transient observers who briefly flicker into existence as a result of quantum or thermal fluctuations. One might then wonder why we are so atypical. I show that tiny changes in physics--for instance, extremely slow variations of fundamental constants--can drastically change this result, and argue that one should be wary of conclusions that rely on exact knowledge of the laws of physics in the very distant future.Comment: 4 pages, LaTeX; v2: added references; v3: more discussion of setting, alternative approaches, now 5 pages; v4: added discussion of the effect of quantum fluctuations on varying constants, appendix added, now 7 pages; v5: new reference, minor correctio